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Status |
Public on Sep 06, 2023 |
Title |
Avil-ChR2 mouse#40 |
Sample type |
SRA |
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Source name |
Brain Cortex
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Organism |
Mus musculus |
Characteristics |
strain: C57BL6 tissue: Cortex age: 7 days gender: female genotype: Advillin-ChR2 positive treatment: blue light
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Treatment protocol |
Mice were exposed to blue light in a chamber from postnatal day p1 to p5, once daily for 1h. Tissue was dissected on p7.
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Growth protocol |
does not apply
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Extracted molecule |
total RNA |
Extraction protocol |
Cortices were removed, flash frozen on dry ice, and total RNA was extracted using Qiagen RNeasy spin columns. Illumina TruSeq mRNA Sample Prep Kit was used with 1 µg of total RNA for the construction of sequencing libraries. Libraries were prepared according to Illumina's instructions. Libraries were prepared according to Illumina's instructions.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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Description |
02_AvilChR08_40
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Data processing |
Sample quality was assessed with demultiplexed fastq.gz files and subsequently the alignment was performed with SeqMan NGen 17 (Lasergene) using the reference genome mm10 provided from UCSC (GRCm38) as template, a minimum read length of 35 bp and automatic adapter trimming. Results were displayed with ArrayStar 17 (Lasergene) including the amount of mapped reads, target length, source length and position, strand, genes and gene IDs, annotated according to the mm10 assembly. The reads were normalized according to EdgeR. Normalized reads were analyzed with ArrayStar 17, which uses general linear models to assess differential expression. Genes were filtered for at least 12 valid values (EdgeR log2 > -5) out of 16 samples to exclude low expression genes. Assembly: mm10 Supplementary files format and content: ELP_EdgeR_36930_allgenes.txt (tab delimited txt file with EdgeR normalized counts for each biological replicate i.e. mouse ) ELPassembly_EdgeR_Valid21695.txt (tab delimited txt file with EdgeR normalized counts of the biological replicates, i.e. mice of filtered valid genes)
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Submission date |
Apr 04, 2022 |
Last update date |
Sep 06, 2023 |
Contact name |
Irmgard Tegeder |
E-mail(s) |
itegeder@hotmail.com
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Phone |
496963017621
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Organization name |
Goethe University Frankfurt
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Department |
Clinical Pharmacology
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Lab |
Clinical Pharmacology
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Street address |
Theodor Stern Kai 7
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City |
Frankfurt |
State/province |
Hessen |
ZIP/Postal code |
60590 |
Country |
Germany |
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Platform ID |
GPL19057 |
Series (1) |
GSE200140 |
Transcriptome analysis by RNA sequencing of the cortical brain in a mouse model of early life pain |
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Relations |
BioSample |
SAMN27292803 |
SRA |
SRX14732623 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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